SDFMOL

SDFMOL is a term used in cheminformatics to denote a molecule object that originates from a Structure Data File (SDF). It is not a formal standard in itself, but a common name in library APIs and tutorials for representing a single molecular entity extracted from an SDF file. An SDFMOL typically encapsulates the core structural data of a molecule, including a list of atoms with element symbols, coordinates, and optional properties such as formal charges or isotopic labels, and a set of bonds with connected atom indices and bond orders. In addition, it may carry data fields read from the SDF's CTAB section, such as compound identifiers, descriptors, or user-defined properties.

Many implementations also track stereochemistry, chirality, ring information, and, in some cases, multiple conformers. Some SDFMOL representations support annotations like atom mapping numbers, formal charges, or custom tags, and provide methods to access, modify, or clone the underlying data.

Common uses include parsing an SDF file to obtain a sequence of SDFMOL objects, performing analyses or substructure searches, converting to other representations (for example SMILES or InChI), and writing molecules back to SDF format. Because SDFMOL is an informal naming convention, the exact API, methods, and storage layout can vary between libraries such as Open Babel, RDKit, or CDK-derived wrappers, while preserving the fundamental idea of a single molecule loaded from an SDF dataset.

See also: Structure Data File, SDF format, chemical informatics.